Sounds like you've eliminated the obvious causes.
After I hypertuned my HEQ5 I found I was getting slight contact between the RA gear and the casing. I could hear a slight grinding when rotating the RA axis which got worse under load. Like you, I'd removed all that thick grease.
There was no obvious problems with the new bearings or my reassembly.
It was clear after working on the mount that it wasn't "high quality". My best guess was that the problem was the result of poor manufacturing and had always been there. The act of removing the thick grease made it apparent.
I identified the location from the visible scratch marks on the RA gear and I used abrasive to remove a small amount of the casing top edge and this fixed the problem.
Chris
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